i took the heads off to change gasgets and found a lot of rust in the #2,3,4 and 5 cylinders i dont know how to clean them out or if there is any way to fix the cylinder walls without putting in bigger pistons so i would like to have some guidance

The repair method depends on the severity of the corrosion and the wear of the cylinders. You'll need to measure to to determine where things stand.
It is possible to run oversize rings if theres light wear or no deep pitting and corrosion. The corrosion can be cleaned with a cylinder bore, hand sanding is not recommended because you dont want to do anything that would get the cylinders out of round.

Hone the cylinders. Dont go crazy tho. It is ok to use a fine grit sand paper on the pistons but only take the top layer of rust off. Clean them with a parts cleaner. I would suggest this stuff I got called bio it is great it is made with orange peels. Be sure to put pleanty of oil 40 wt on the pistons and the cylinder walls this will help protect against corosion till you get things put back togather. Please dont take a grinder to the pistons please. Also it only should take about 3 up and down motions with the hone if that dont get it take it and have it bored. We do this on the engines we repair. It should work fine for you. Be sure you mike everything and make sure it is with in specs.

Just curious, but how do you get much rust in a truck that is being used regularly? I can see how a coolant lea-head or intake gaskets- would dump water/coolant in it(but combustion gases are filled with water anyway?), but wouldn't the oil sorta prevent much rust-and the rings scrape the rust off every time it is run??

You'd be surprised how fast the internals of an engine develop corrosion when subjected to moisture, if the rings are working properly there shouldnt be any oil in the top of the cylinder after the down stroke and heat treated metals corrode within minutes.

sorry bout the long wait college is getting started again so im up to my neck in work and school and dead cars

i filled the rusted cylinders with Marvel mystery oil and hoping that will help
most of the rust wasn't very bad so i cleaned out what i saw with an steel wool pad now i will probably try and track down a hone tool however

as i said earlier i thought it was head gaskets but there dosent seem to be any rust on the gaskets except were the bolts are so i dont thing the gaskets are messed up which means either heads or the block (i think, somebody say something if im wrong) does any one know were i can get that metal spray stuff to check the heads for cracks

EDIT: one more thing we replaced heads and gaskets before and this time the freeze plug blew so we lost all coolant and that is what started the problem after that we procrastenated and it took about a year for us to get back to working on the truck so this wasnt overnight